中科院武汉病毒研究所石正丽研究员带领的研究团队采用宏基因组学方法，对我国蝙蝠肠道病毒首次进行了系统研究，结果发表在《病毒学杂志》（Journal of Virology）上（2012， 86(8)：4620. DOI： 10.1128/JVI.06671-11）。
蝙蝠是哺乳动物中仅次于啮齿目动物的第二大类群，也是已知的唯一具有飞翔能力的哺乳动物。如今，越来越多的证据表明蝙蝠是多种新发病毒的自然宿主，有些蝙蝠来源的病毒会导致人类严重的病毒性疾病，如“著名”的亨德拉病毒、尼帕病毒、狂犬病毒、埃博拉病毒、马尔堡病毒等。
病毒分离一直是最为直接的病毒研究方法，但是在现有实验室条件下很多病毒难以分离；由于病毒之间缺少保守的基因标记，特异性PCR检测难以系统研究样品中的所有病毒（病毒组，Virome）。而病毒核酸序列的随机扩增（sequence-independent amplification），结合高通量测序技术（high-throughput sequencing，如Solexa等）可以全面研究某一生境下的病毒组。
石正丽研究员领导的研究小组用病毒宏基因组学方法，系统地研究了中国6个不同地区的食虫蝙蝠粪便样品中的病毒。结果显示，蝙蝠肠道中存在有大量浓核病毒（densoviruses）、双顺反子病毒（dicistroviruses）、冠状病毒（coronaviruses）、细小病毒（parvoviruses）、烟草花叶病毒（tobamoviruses）等。这些病毒的宿主涵盖了脊椎动物、无脊椎动物、植物。此外，本研究发现的大多数病毒序列与已知的病毒基因组（或蛋白序列）同源性很低，证明蝙蝠肠道有大量新的昆虫病毒、哺乳动物病毒，推测蝙蝠在这些病毒的传播中起着重要的作用。
本研究首次初步揭示了我国某些蝙蝠群体中的病毒组，对指导未来新病毒的发现和分离有重要意义。（生物谷Bioon.com）
doi:10.1128/JVI.06671-11
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Metagenomic Analysis of Viruses from the Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China
Xingyi Ge1, Yan Li1, Xinglou Yang1, Huajun Zhang1, Peng Zhou1, Yunzhi Zhang2 and Zhengli Shi1,*
Increasing data indicate that bats harbor diverse viruses, some of which cause severe human diseases. In this study, sequence-independent amplification and high-throughput sequencing (Solexa) were applied to the metagenomic analysis of viruses in bat fecal samples collected from 6 locations in China. A total of 8,746,417 reads with a length of 306,124,595 bp were obtained. Among these reads, 13,541 (0.15%) had similarity to phage sequences and 9,170 (0.1%) had similarity to eukaryotic virus sequences. A total of 129 assembled contigs (>100nt) were constructed and compared with GenBank: 32 contigs were related to phages, and 97 were related to eukaryotic viruses. The most frequent reads and contigs related to eukaryotic viruses were homologous to densoviruses, dicistroviruses, coronaviruses, parvoviruses and tobamoviruses, a range that includes viruses from invertebrates, vertebrates and plants. Most of the contigs had low identities to known viral genomic or protein sequences, suggesting that a large number of novel and genetically diverse insect viruses as well as putative mammalian viruses are transmitted by bats in China. This study provides the first preliminary understanding of the virome of some bat populations in China, which may guide the discovery and isolation of novel viruses in the future.
